Planting winter cover crops into corn-soybean rotations is a potential approach for reducing subsurface drainage and nitrate-nitrogen (NO3-N) loss. However, the long-term impact of this practice needs investigation. We evaluated the RZWQM2 model against comprehensive field data (2005-2009) in Iowa and used this model to study the long-term (1970-2009) hydrologic and nitrogen cycling effects of a winter cover crop within a corn-soybean rotation. The calibrated RZWQM2 model satisfactorily simulated crop yield, biomass, and N uptake with percent error (PE) within ±15% and relative root mean square error (RRMSE) <30% except for soybean biomass and rye N uptake. Daily and annual drainage and annual NO3-N loss were simulated satisfactorily, with Nash-Sutcliffe efficiency (NSE) >0.50, ratio of RMSE to standard error (RSR) <0.70, and percent bias (PBIAS) within ±25% except for the overestimation of annual drainage and NO3-N in CTRL2. The simulation in soil water storage was unsatisfactory but comparable to other studies. Long-term simulations showed that adding rye as a winter cover crop reduced annual subsurface drainage and NO3-N loss by 11% (2.9 cm) and 22% (11.8 kg N ha-1), respectively, and increased annual ET by 5% (2.9 cm). Results suggest that introducing winter rye cover crops to corn-soybean rotations is a promising approach to reduce N loss from subsurface drained agricultural systems. However, simulated N immobilization under the winter cover crop was not increased, which is inconsistent with a lysimeter study previously reported in the literature. Therefore, further research is needed to refine the simulation of immobilization in cover crop systems using RZWQM2 under a wider range of weather conditions.